Lost in Tokenization: Context as the Key to Unlocking Biomolecular Understanding in Scientific LLMs

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at github.com/opendatalab-raise-dev/CoKE.

Traffic Sign Interpretation in Real Road Scene

Most existing traffic sign-related works are dedicated to detecting and recognizing part of traffic signs individually, which fails to analyze the global semantic logic among signs and may convey inaccurate traffic instruction. Following the above issues, we propose a traffic sign interpretation (TSI) task, which aims to interpret global semantic interrelated traffic signs (e.g.,~driving instruction-related texts, symbols, and guide panels) into a natural language for providing accurate instruction support to autonomous or assistant driving. Meanwhile, we design a multi-task learning architecture for TSI, which is responsible for detecting and recognizing various traffic signs and interpreting them into a natural language like a human. Furthermore, the absence of a public TSI available dataset prompts us to build a traffic sign interpretation dataset, namely TSI-CN. The dataset consists of real road scene images, which are captured from the highway and the urban way in China from a driver's perspective. It contains rich location labels of texts, symbols, and guide panels, and the corresponding natural language description labels. Experiments on TSI-CN demonstrate that the TSI task is achievable and the TSI architecture can interpret traffic signs from scenes successfully even if there is a complex semantic logic among signs. The TSI-CN dataset and the source code of the TSI architecture will be publicly available after the revision process.